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After doing a clean install of Mint 13/Cinnamon, and then restoring my home directory and apps, all is well except for one annoying thing: When I run Jitsi (a Java app), "JavaEmbeddedFrame" appears in my task bar. This did not happen under Mint 12/Cinnamon. How can I make it go away? I tried switching to Oracle/Sun jre 7, but that didn't change anything.

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As this still was an issue for me – Ubuntu 17.10 artful with Cinnamon 3.4.6 from Ubuntu's default software sources, using "Icing Task Manager" as my task bar/window list –, here's a "fix" (rather a workaround) that hopefully works for others, too. This fix should not be limited to Cinnamon, though. Certainly, neither issue nor fix are limited to Linux Mint. This should work in any Desktop Environment or applet that makes use of the *.desktop files in /usr/share/applications/ and ~/.local/share/applications/ for applications menu and/or docks/task list/task bar.

Create a plain-text file in the following sub-folder within your $HOME directory (create sub-folders if necessary – that's what the -p switch below is for). The name of the file itself does not really matter, the filename extension is the important part. For the sake of this example, let's call the file hide-JavaEmbeddedFrame.desktop. Run the following two commands, one after the other, in a terminal window as your normal user: Of course, instead of gedit you can use whichever text editor you feel comfortable with or that is installed on your system, such as nano/pico, vim, emacs, pluma, sublime-text, ...

Paste the following content into the new and empty file opened by your text editor, save the file and exit the editor:
I think, the lines starting with Name= and Comment= are, in fact, optional, as this information should not be displayed or used anywhere (prohibited by NoDisplay=true). However, I recommend leaving these lines there in case you stumble upon this long-forgotten file in a few months or years and wonder what the heck it is good for. Of course, you can adjust their text to your liking, translate it to your language, whatever you like. The other lines are necessary as is (well, the Terminal= line might not be, but I really don't feel like diving into the horrible and incomplete documentation of .desktop files right now ).

In case of Cinnamon, you might have to restart Cinnamon (Ctrl+Alt+Esc or Alt+F2 and enter r or Alt+F2 and enter cinnamon --replace or right-click on panel > Troubleshoot > Restart Cinnamon). Same goes for other Desktop Environments: you might have to restart them for the changes to take effect. Or simply log out and back in again.

If this fix works for you, and you want to apply it system-wide – hence, for all users on the machine –, simply move the hide-JavaEmbeddedFrame.desktop file as root to the /usr/share/applications/ folder.